{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/checksum.txt"],"Csv":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/171225_FAF2_ND_IA_final_peptide.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/211025_P97_UN_FAF2_D_IA_final_peptide.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/221025_P97_UN_FAF2_D_LOW_IA_final_peptide.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/171225_FAF2_ND_2_IA_final_peptide.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/231025_P97_UN_FAF2_ATPyS_ND1_IA_final_peptide.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/221025_P97_UN_FAF2_D_LOW2_IA_final_peptide.csv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/171225_FAF2_ND.raw.zip"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/FAF2_complex.hdx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD073479/p97_complex.hdx"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["gmasson001@dundee.ac.uk"],"submitter":["Glenn Masson"],"technology_type":["HDMSE","Mass Spectrometry"],"software":["Not available"],"submitter_keywords":["Hdx-ms","Faf2","P97"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073479"],"sample_protocol":["To address how adaptor proteins impact human p97 activity, we here employ in vitro reconstitution and a focused biochemical screen to identify adaptors that enhance unfoldase activity of human p97 in the presence of UFD1-NPL4. Of the adaptors tested, Fas-associated factor 2 (FAF2/UBXD8), a UBX domain adaptor protein, shows the strongest effect on unfolding by p97-UFD1-NPL4 complex. Through biochemical and structural analysis, we define the molecular features that underpin FAF2-mediated stimulation. Based on these insights, we employ computational protein design to engineer de novo mini-proteins that mimic FAF2 function within novel protein scaffolds to potently activate p97.  Our work reveals how the unfoldase activity of p97 can be enhanced by additional adaptors, an adaptive feature we believe is important to unfold misfolded proteins, extract proteins from the membrane and tightly bound multiprotein complexes."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["HDX-MS data acquisition Samples were rapidly thawed at room temperature and then injected into automated HDX-MS fluidics and UPLC manager system (Waters). Samples were loaded into a 50 µl loop and then subsequently digested using a Waters Enzymate BEH Pepsin Column (Part No. 186007233) in a 0.1% Formic Acid solution with a flow rate of 200 µl/min at 20°C. Peptic peptides then flowed onto a Waters ACQUITY UPLC BEH C18 VanGuard Pre-Column at 1°C (Part No. 186003975). After digestion, the flow path was changed to elute the peptides via a Waters ACQUITY UPLC BEH C18 1.7 µm 1.0 × 100 mm reverse phase column (Part No. 186002346). A gradient from 0-85% 0.1% Formic Acid/ Acetonitrile, conducted at 1°C with a 40 µl/min flowrate, was used to elute deuterated peptides which were then ionised using an ESI source. Mass spectrometry data were collected using a Waters Select Series cIMS instrument, from a 50–2,000 m/z range with the instrument in HDMSe mode. A single pass of the cyclic ion mobility separator (with a cycle time of 47 ms) was conducted. A blank sample of protein dilution buffer with quench was run between samples, and carryover was routinely checked to be <1% intensity of the prior sample. HDX-MS data analysis Peptide sequence identification was conducted using Protein Lynx Global Server (Waters), searching against a database of the protein complex, common contaminants, porcine pepsin, and previous project’s sequences. Search criteria includes S/T/Y phosphorylation.  Minimum inclusion criteria were a minimum intensity of 5000 counts, minimum sequence length 5, maximum sequence length 35, a minimum of three fragment ions, a minimum of 0.1 products per amino acid, a minimum score of 5.0, a maximum MH+Error of 10 ppm. Subsequent analysis and determination of deuteration values conducted using HDExaminer (Sierra Analytics/Trajan). Experimental design, data acquisition, analysis and reporting are in line with the community agreed recommendations"],"omics_type":["Proteomics"],"labhead":["Glenn Masson"],"instrument_platform":[""],"labhead_affiliation":["School of Medicine, University of Dundee"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["gmasson001@dundee.ac.uk"],"publication":["Not available"],"curator_keywords":["Hydrogen deuterium exchange (hdx-ms)"],"submitter_affiliation":["University of Dundee"],"submitter_country":["United Kingdom"],"additional_accession":[]},"is_claimable":false,"name":"FAF2 enhances unfoldase activity of mammalian p97-UFD1-NPL4 complex enabling rational design of p97","description":"To address how adaptor proteins impact human p97 activity, we here employ in vitro reconstitution and a focused biochemical screen to identify adaptors that enhance unfoldase activity of human p97 in the presence of UFD1-NPL4. Of the adaptors tested, Fas-associated factor 2 (FAF2/UBXD8), a UBX domain adaptor protein, shows the strongest effect on unfolding by p97-UFD1-NPL4 complex. Through biochemical and structural analysis, we define the molecular features that underpin FAF2-mediated stimulation. Based on these insights, we employ computational protein design to engineer de novo mini-proteins that mimic FAF2 function within novel protein scaffolds to potently activate p97.  Our work reveals how the unfoldase activity of p97 can be enhanced by additional adaptors, an adaptive feature we believe is important to unfold misfolded proteins, extract proteins from the membrane and tightly bound multiprotein complexes.","dates":{"publication":"2026-07-28","submission":"2026-01-23"},"accession":"PXD073479","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:8479","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:630","NEWT:334747","NEWT:61235","NEWT:15368","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:469008","NEWT:260707","NEWT:256318","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","N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